A new government plan to protect the Great Barrier Reef has been signed as a new report paints a grim picture of the icon, warning of declines in significant species and outbreaks of disease.

The Great Barrier Reef Outlook report - the first and most comprehensive of its kind - was released on Wednesday as Queensland Premier Anna Bligh and federal Environment Minister Peter Garrett signed a new reef plan to improve the water quality for the natural wonder.

The report identifies climate change, continued declining water quality from catchment run-off, loss of coastal habitats from development and remaining impacts from fishing and illegal fishing as the key issues undermining the resilience of the reef.

It said damage to mangroves, increasing algae on coral reefs, ocean acidification and coral bleaching were already evident.

``While populations of almost all marine species are intact and there are no records of extinctions, some ecologically important species, such as dugongs, marine turtles, seabirds, black teatfish and some sharks, have declined significantly,'' it said.

''... Disease in corals and pest outbreaks of crown-of-thorns starfish and cyanobacteria appear to be becoming more frequent and more serious.''

It follows a report a year ago which found agricultural run-off was killing the Great Barrier Reef and that some sections were already irreversibly damaged, prompting a government promise to toughen regulations for farmers.

New government targets aim to reduce agricultural run-off by half and see 80 per cent of agricultural enterprises and 50 per cent of grain enterprises adopt land management practices to reduce run-off, all by 2013.

And a minimum 20 per cent reduction in sediment loads is planned by 2020.

Among the measures, $76 million was available for farmers to help them change their practices faster, Mr Garret said.

``Farmers are already engaging in improving their practices,'' he told reporters in Brisbane.

``What this particular support enables them to do is to do more and to do it quickly.''

Ms Bligh said the reef was in danger of being ``loved to death''.

Two million people visited the coast between Bundaberg and Cairns each year, spending more than $5 million and underpinning 50,000 jobs in the tourism industry alone, she said.

Fisheries contribute a further $290 million annually to the economy.

``We simply cannot afford to stand back and do nothing when we know it is at such risk,'' Ms Bligh said.

WWF spokesman Nick Heath welcomed the new goals but said more needed to be done.

``It's really sad,'' he told reporters in Brisbane.

``We are seeing the reef on the brink of a catastrophe and we are going to have to see far faster action, far deeper cuts in our climate emissions from both our federal and state governments than we've seen to date.

``This is a trigger for more action, not words.''

He said land clearing and coal-fired power stations had to be banned, solar energy embraced, shark fishing reduced and carbon emissions strongly tackled.

Mr Heath said parts of the reef were already dying and would be catastrophically damaged within five years if significant action was not taken in the next 12 months.